3O6F

Crystal structure of a human autoimmune TCR MS2-3C8 bound to MHC class II self-ligand MBP/HLA-DR4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structure of a TCR with high affinity for self-antigen reveals basis for escape from negative selection.

Yin, Y., Li, Y., Kerzic, M.C., Martin, R., Mariuzza, R.A.

(2011) Embo J. 30: 1137-1148

  • DOI: 10.1038/emboj.2011.21

  • PubMed Abstract: 

    • The failure to eliminate self-reactive T cells during negative selection is a prerequisite for autoimmunity. To escape deletion, autoreactive T-cell receptors (TCRs) may form unstable complexes with self-peptide-MHC by adopting suboptimal binding top ...

    The failure to eliminate self-reactive T cells during negative selection is a prerequisite for autoimmunity. To escape deletion, autoreactive T-cell receptors (TCRs) may form unstable complexes with self-peptide-MHC by adopting suboptimal binding topologies compared with anti-microbial TCRs. Alternatively, escape can occur by weak binding between self-peptides and MHC. We determined the structure of a human autoimmune TCR (MS2-3C8) bound to a self-peptide from myelin basic protein (MBP) and the multiple sclerosis-associated MHC molecule HLA-DR4. MBP is loosely accommodated in the HLA-DR4-binding groove, accounting for its low affinity. Conversely, MS2-3C8 binds MBP-DR4 as tightly as the most avid anti-microbial TCRs. MS2-3C8 engages self-antigen via a docking mode that resembles the optimal topology of anti-foreign TCRs, but is distinct from that of other autoreactive TCRs. Combined with a unique CDR3β conformation, this docking mode compensates for the weak binding of MBP to HLA-DR4 by maximizing interactions between MS2-3C8 and MBP. Thus, the MS2-3C8-MBP-DR4 complex reveals the basis for an alternative strategy whereby autoreactive T cells escape negative selection, yet retain the ability to initiate autoimmunity.

    Organizational Affiliation: 

    Institute for Bioscience and Biotechnology Research, University of Maryland, WM Keck Laboratory for Structural Biology, Rockville, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A, E
182Homo sapiensGene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DRB1-4 beta chain
B, F
221Homo sapiensGene Names: HLA-DRB1
Find proteins for P13760 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P13760
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor alpha chain C region
C, G
206Homo sapiensGene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor beta-1 chain C region
D, H
245Homo sapiensMutations: C189S
Gene Names: TRBC2 (TCRBC2)
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.480α = 90.00
b = 218.403β = 90.00
c = 98.412γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-09-07
    Type: Database references
  • Version 1.3: 2017-08-09
    Type: Advisory, Refinement description, Source and taxonomy